ALBERT

Description: Non-structural carbohydrates (NSC) in plant tissue are frequently quantified to make inferences about plant responses to environmental conditions. Laboratories publishing estimates of NSC of woody plants use many different methods to evaluate NSC. We asked whether NSC estimates in the recent literature could be quantitatively compared among studies. We also asked whether any differences among laboratories were related to the extraction and quantification methods used to determine starch and sugar concentrations. These questions were addressed by sending sub-samples collected from five woody plant tissues, which varied in NSC content and chemical composition, to 29 laboratories. Each laboratory analyzed the samples with their laboratory-specific protocols, based on recent publications, to determine concentrations of soluble sugars, starch and their sum, total NSC. Laboratory estimates differed substantially for all samples. For example, estimates for Eucalyptus globulus leaves (EGL) varied from 23 to 116 (mean = 56) mg g –1 for soluble sugars, 6–533 (mean = 94) mg g –1 for starch and 53–649 (mean = 153) mg g –1 for total NSC. Mixed model analysis of variance showed that much of the variability among laboratories was unrelated to the categories we used for extraction and quantification methods (method category R 2 = 0.05–0.12 for soluble sugars, 0.10–0.33 for starch and 0.01–0.09 for total NSC). For EGL, the difference between the highest and lowest least squares means for categories in the mixed model analysis was 33 mg g –1 for total NSC, compared with the range of laboratory estimates of 596 mg g –1 . Laboratories were reasonably consistent in their ranks of estimates among tissues for starch ( r = 0.41–0.91), but less so for total NSC ( r = 0.45–0.84) and soluble sugars ( r = 0.11–0.83). Our results show that NSC estimates for woody plant tissues cannot be compared among laboratories. The relative changes in NSC between treatments measured within a laboratory may be comparable within and between laboratories, especially for starch. To obtain comparable NSC estimates, we suggest that users can either adopt the reference method given in this publication, or report estimates for a portion of samples using the reference method, and report estimates for a standard reference material. Researchers interested in NSC estimates should work to identify and adopt standard methods.

Description: For development of advanced materials, characterization using a scanning transmission electron microscope (STEM) including analysis via X-ray energy-dispersive spectrometry and electron energy-loss spectrometry is essential. Recent advances in aberration-corrected instruments have offered large-scale data acquisition at a high resolution for limited acquisition times both in imaging and in analysis. Further advanced procedures are required to analyze such large-scale datasets more efficiently including quantification. In addition, more simplified tuning procedures are crucial to the best possible resolution in the latest aberration-corrected instruments. In this review article, several approaches to perform advanced electron microscopy, which the author has been developing with his colleague, are described as ‘Microscopy Hacks’. These are (i) quantification and elemental/chemical-imaging procedures, (ii) advanced statistical approaches to handle large-scale datasets and (iii) instrument characterization and tuning procedures including the latest development of an ad hoc autotuning procedure for aberration-corrected STEM imaging.

Description: We present the results of an imaging observation campaign conducted with the Subaru Telescope adaptive optics system (IRCS+AO188) on 28 gravitationally lensed quasars and candidates (23 doubles, 1 quad, 1 possible triple, and 3 candidates) from the SDSS Quasar Lens Search. We develop a novel modelling technique that fits analytical and hybrid point spread functions (PSFs), while simultaneously measuring the relative astrometry, photometry, as well as the lens galaxy morphology. We account for systematics by simulating the observed systems using separately observed PSF stars. The measured relative astrometry is comparable with that typically achieved with the Hubble Space Telescope , even after marginalizing over the PSF uncertainty. We model for the first time the quasar host galaxies in five systems, without a priori knowledge of the PSF, and show that their luminosities follow the known correlation with the mass of the supermassive black hole. For each system, we obtain mass models far more accurate than those previously published from low-resolution data, and we show that in our sample of lensing galaxies the observed light profile is more elliptical than the mass, for ellipticity 0.25. We also identify eight doubles for which the sources of external and internal shear are more reliably separated, and should therefore be prioritized in monitoring campaigns aimed at measuring time delays in order to infer the Hubble constant.

Description: Despite many studies on avian phylogenetics in recent decades that used morphology, mitochondrial genomes, and/or nuclear genes, the phylogenetic positions of several birds (e.g., storks) remain unsettled. In addition to the aforementioned approaches, analysis of retroposon insertions, which are nearly homoplasy-free phylogenetic markers, has also been used in avian phylogenetics. However, the first step in the analysis of retroposon insertions, that is, isolation of retroposons from genomic libraries, is a costly and time-consuming procedure. Therefore, we developed a high-throughput and cost-effective protocol to collect retroposon insertion information based on next-generation sequencing technology, which we call here the STRONG ( S creening of Tr ansposons O btained by N ext G eneration Sequencing) method, and applied it to 3 waterbird species, for which we identified 35,470 loci containing chicken repeat 1 retroposons (CR1). Our analysis of the presence/absence of 30 CR1 insertions demonstrated the intra- and interordinal phylogenetic relationships in the waterbird assemblage, namely 1) Loons diverged first among the waterbirds, 2) penguins (Sphenisciformes) and petrels (Procellariiformes) diverged next, and 3) among the remaining families of waterbirds traditionally classified in Ciconiiformes/Pelecaniformes, storks (Ciconiidae) diverged first. Furthermore, our genome-scale, in silico retroposon analysis based on published genome data uncovered a complex divergence history among pelican, heron, and ibis lineages, presumably involving ancient interspecies hybridization between the heron and ibis lineages. Thus, our retroposon-based waterbird phylogeny and the established phylogenetic position of storks will help to understand the evolutionary processes of aquatic adaptation and related morphological convergent evolution.

Description: The hybrid larch F 1 ( Larix gmelinii var. japonica x Larix kaempferi ) is considered one of the most important tree species not only for timber production but also as an afforestation material for severe conditions such as infertile soil. To predict the ability of hybrid larch F 1 as an afforestation material under potential climates in the future, it is important to understand the response of hybrid larch F 1 to elevated CO 2 concentration ([CO 2 ]) under low nutrient availability. Three-year-old seedlings of hybrid larch F 1 were grown under two different levels of [CO 2 ], 360 (ambient) and 720 µmol mol –1 (elevated), in combination with two different levels of nitrogen (N) supply (0 and 30 kg ha –1 ) for one growing season. Elevated [CO 2 ] reduced the maximum rates of carboxylation and electron transport in the needles. Net photosynthetic rates at growth [CO 2 ] (i.e., 360 and 720 µmol mol –1 for ambient and elevated treatment, respectively) did not differ between the two CO 2 treatments. Reductions in N content and N use efficiency to perform photosynthetic functions owing to the deficiency of nutrients other than N, such as P and K, and/or increase in cell wall mass were considered factors of photosynthetic down-regulation under elevated [CO 2 ], whereas stomatal closure little affected the photosynthetic down-regulation. Although we observed strong down-regulation of photosynthesis, the dry matter increase of hybrid larch F 1 seedlings was enhanced under elevated [CO 2 ]. This is mainly attributable to the increase in the amount of needles on increasing the number of sylleptic branches. These results suggest that elevated CO 2 may increase the growth of hybrid larch F 1 even under low nutrient availability, and that this increase may be regulated by changes in both crown architecture and needle photosynthesis, which is mainly affected not by stomatal limitation but by biochemical limitation.

Description: We examined the effects of photoperiod, wavelength and light fluence rate on diurnal vertical migration (DVM) cycle in a coastal raphidophyte, Chattonella antiqua . We first observed the DVM under different combinations of light–dark (LD) cycles and light spectra. Under continuous white, UV-A or blue light, DVM followed the LD cycle established during the white light pre-conditioning, for one cycle, and then became arrhythmic. Under red light, however, the DVM rhythms under the different LD regimes continued approximately as during pre-conditioning. When C. antiqua cultured under continuous red light was exposed to a 2-h pulse of blue light at the beginning or end of artificial ‘night’, the DVM was delayed or advanced, respectively. The fluence rate–response curve indicates a blue-light threshold of 10 –2 μmol photons m –2 s –1 for the DVM phase shift. The equal-quantum action spectra for phase shift peaked in the UV-A/blue region (360–480 nm), which is the part of the light spectrum most transmitted in its natural habitat. We show that C. antiqua can sense the weak blue component of sunlight throughout its depth range, allowing it to cue its DVM to the day–night cycle regardless of weather and transparency.

Description: Rapid human urbanization can have strong and varied impacts on the behavior and fitness of wild animals. The "credit-card hypothesis" predicts that low predation and high food predictability in cities lead to the presence of many weak competitors in urban populations. However, no experimental studies to date have found support for this hypothesis. Here, we studied the relationship between urbanization and aggressiveness in males of a widespread North American songbird (the house finch, Haemorhous mexicanus ) while taking into account the degree of sexual signal elaboration (plumage coloration), which is known to impact competitive outcomes. In paired laboratory experiments, we found that colorful urban males were less aggressive than drab urban males, whereas there was no significant difference in aggressiveness between colorful and drab rural males. Moreover, we found that colorful urban males were less aggressive than colorful rural males, whereas there was no significant difference in aggressiveness between drab urban and drab rural males. In 4-bird trials (i.e., trials with colorful and drab males from both urban and rural environments), we found that colorful urban males were consistently less aggressive than all others. Taken together, these results support the credit-card hypothesis and the idea that plumage color is an important predictor of social status in urban environments. Finally, in a model-presentation study, we found that urban males with lower body condition avoided drab male models. Urban settings, along with the social and foraging conditions they create, may exert novel selection pressures that shape the competitiveness and status signaling systems of animals.

Description: Ochratoxin A (OTA) is a carcinogen targeting proximal tubules at the renal outer medulla (ROM) in rodents. We previously reported that OTA increased mutant frequencies of the red / gam gene (Spi – ), primarily deletion mutations. In the present study, Spi – assays and mutation spectrum analyses in the Spi – mutants were performed using additional samples collected in our previous study. Spi – assay results were similar to those in our previous study, revealing large (〉1kb) deletion mutations in the red/gam gene. To clarify the molecular progression from DNA damage to gene mutations, in vivo comet assays and analysis of DNA damage/repair-related mRNA and/or protein expression was performed using the ROM of gpt delta rats treated with OTA at 70, 210 or 630 µg/kg/day by gavage for 4 weeks. Western blotting and immunohistochemical staining demonstrated that OTA increased -H2AX expression specifically at the carcinogenic target site. In view of the results of comet assays, we suspected that OTA was capable of inducing double-strand breaks (DSBs) at the target sites. mRNA and/or protein expression levels of homologous recombination (HR) repair-related genes ( Rad51 , Rad18 and Brip1 ), but not nonhomologous end joining-related genes, were increased in response to OTA in a dose-dependent manner. Moreover, dramatic increases in the expression of genes involved in G 2 /M arrest ( Chek1 and Wee1 ) and S/G 2 phase ( Ccna2 and Cdk1 ) were observed, suggesting that DSBs induced by OTA were repaired predominantly by HR repair, possibly due to OTA-specific cell cycle regulation, consequently producing large deletion mutations at the carcinogenic target site.

Description: The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase ( http://genome.microbedb.jp/cyanobase ), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface for large genomic data to include the use of semantic web technologies and JBrowse and have extended community-based reannotation resources through the re-annotation of Synechocystis sp. PCC 6803 by the cyanobacterial research community. These updates have markedly improved CyanoBase, providing cyanobacterial genome annotations as references for cyanobacterial research.